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Illumina Unveils Mini Targeted Sequencer, Semiconductor Sequencing Project at JP Morgan Conference

SAN FRANCISCO (GenomeWeb) – Illumina today announced two new next-generation sequencing platforms, a targeted sequencing system called MiniSeq and a semiconductor sequencer that is still under development.

Illumina disclosed the initiatives during a presentation at the JP Morgan Healthcare conference held here today. During the presentation, Illumina CEO Jay Flatley also announced a new genotyping array called Infinium XT; a partnership with Bio-Rad to develop a single-cell sequencing workflow; preliminary estimates of its fourth-quarter 2015 revenues; and an update on existing products. The presentation followed the company's announcement on Sunday that it has launched a new company called Grail to develop a next-generation sequencing test for early cancer detection from patient blood samples.

The MiniSeq system, which is based on Illumina's current sequencing technology, will begin shipping early this quarter and has a list price of $49,500. It can perform a variety of targeted DNA and RNA applications, from single-gene to pathway sequencing, and promises "all-in" prices, including library prep and sequencing, of $200 to $300 per sample, Flatley said during the JP Morgan presentation.

Illumina is commercializing the system as part of a complete workflow, from library preparation to onboard data analysis, and the platform can stream data to Illumina's BaseSpace environment.

Flatley said that MiniSeq is 44 percent smaller than the MiSeq instrument and combines the "best of engineering" components from MiSeq and the NextSeq instruments. MiniSeq will have one optical module and one pumping system, and will incorporate the two-channel chemistry of the NextSeq, but on a flow cell and with a load mechanism that is more similar to the MiSeq. The instrument will have an output of 7.5 gigabases for paired-end 2x150 base reads and can generate up to 50 million reads for counting applications, Flatley said.

He added that MiniSeq is an "important addition to the desktop sequencing lineup" and will also "open up a new market segment" in the "lower-priced, lower-throughput" space, which includes molecular pathologists, translational researchers, and smaller laboratories.

In addition, under an initiative called Project Firefly, Illumina is developing a semiconductor sequencing system with two modules that will couple its sequencing-by-synthesis chemistry with a semiconductor chip.

The technology will be based off of CMOS sensor technology that Illumina acquired when it bought Avantome in 2008. Flatley said that Avantome's original technology required emulsion PCR, and Illumina "didn't want to market a product that required that." Since then, the firm has been working to figure out a way to combine SBS chemistry on a semiconductor chip.

To do that, Flatley said that Illumina is using a one-channel version of SBS chemistry — down from the two-channel version used in the NextSeq and the four-channel version it originally developed. In addition, the firm "borrowed from its patterned flow cell" technology to enable nanowells that enable patterned clusters of DNA deposition.

It is expected to be commercialized in the second half of 2017, with a list price of less than $30,000 for both modules. The system will have an output of about 1.2 gigabases per run and be "the most integrated sequencer ever developed," according to the company. Consumables costs per sample will be near $100.

The library preparation module, which uses digital fluidics technology, can process eight samples in parallel on a cartridge. The sequencing module, which uses a separate cartridge, deploys the SBS chemistry on a single channel, using a semiconductor chip, and sends the sequencing data to BaseSpace for analysis. Library prep will take 3.5 hours, while sequencing will take between 3.5 hours and 13 hours depending on the application, Flatley said.

Illumina said that the new system "will be superior to competing semiconductor-based sequencing systems with a raw error rate of less than one percent [and] data quality comparable to that of a HiSeqX Sequencing System" and will "be ideal for numerous markets including academic research, oncology, infectious disease, inherited disease, and reproductive health."

Flatley said that Illumina would be partnering with third-party developers on applications and said that Project Firefly would require "substantial investment" in 2016, which was why the firm decided to disclose its plans now.

Meantime, Infinium XT is a 96-sample BeadChip array for genotyping 1 million samples or more per year, testing up to 50,000 markers per sample. The chip, which Illumina said will be particularly suited for agrigenomics but also for human biobank and personalized medicine applications, will start shipping in the third quarter of this year.

Preliminary earnings

Flatley also provided a preliminary revenue forecast for the fourth quarter and full year of 2015. The firm expects Q4 2015 revenues of $590 million, a 15 percent year-over-year increase, and ahead of the consensus analysts' estimate of $571.2 million, driven by strength in the desktop sequencing market, including record sales of NextSeq and strong MiSeq sales, Flatley said. For the full year, Flatley said revenues would be around $2.2 billion, a 19 percent year-over-year increase, and in line with the current Wall St. estimate.

NextSeq was a "star performer" in Q4 2015, Flatley said, adding that the firm has now installed 1,150 NextSeq systems worldwide. In addition, he said the firm has installed around 4,300 MiSeq instruments, 2,050 HiSeq systems, and 300 HiSeq X units.

Flatley noted that Illumina is increasingly moving to develop complete "sample-to-answer" products, such as its NeoPrep library prep system, its TruSight HLA product, and the MiSeq FGx system. The sequencing markets for HLA typing and forensics represent $250 million and $500 million opportunities, respectively, he said. In 2016, Flatley said that Illumina expects to double placements of its MiSeq FGx system from the 45 it has shipped this year.

In 2016, Flatley predicted that Illumina's revenues would grow 16 percent and that the firm would realize an EPS in the range of $3.55 to $3.65. Also, in the second quarter of 2016, Illumina plans to launch a CE-IVD marked version of VeriSeq NIPT. He added that the firm is still committed toward working with the US Food and Drug Administration on gaining clearance for its NIPT, but said that "ambiguity" from the US Food and Drug Administration has "slowed progress." He also predicted that 2016 would see a shift toward payors reimbursing for tests for women with average-risk pregnancies and that reimbursement for such pregnancies would likely fall between $400 and $500.